The project was top of Premier Annastacia Palaszczuk's funding wish list, but there was no place for it in the $5.2 billion allocated to state infrastructure in Tuesday's federal budget.
Ms Palaszczuk's Labor government has already committed to bankrolling the $5.4 billion rail line on its own, having failed to secure money from Malcolm Turnbull.
The Labor leader on Monday accused the prime minister of ignoring the state's "number one infrastructure project" in favour of NSW and Victoria.
Yet Queensland was the second biggest winner in the budget, with one-fifth of the federal government's $24.5 billion spend on roads and rail going to the Sunshine State.
A majority - $3.3 billion - has been slated for upgrades along the Bruce Highway, including sections between Cooroy and Curra, and Pine River and Caloundra.
A further $1 billion is being promised for the M1 Pacific Highway, $390 million to duplicate a section of the North Coast line, and $300 million for the Brisbane Metro.
It will also get a share of a $1.5 billion fund for roads across Northern Australia, and money to improve parts of the Outback Way to Winton.
The Palaszczuk government's call for help to fund the Rockhampton levee and Townsville Port upgrade were left unanswered.
As announced in April, Canberra has committed more than $500 million to help restore and protect the Great Barrier Reef.
The five-year package, combined with philanthropic and other funding sources, is aimed at improving the reef's water quality, controlling the crown-of-thorns starfish and boosting science for reef restoration.
The federal government will also continue to fund a website to help North Queensland residents compare home insurance policies and premiums.
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WHAT'S IN THE BUDGET FOR QUEENSLAND
* $3.3 billion for upgrades along the Bruce Highway, including sections between Cooroy and Curra and Pine River to Caloundra
* $1 billion for the M1 Pacific Highway between Eight Mile Plains and Daisy Hill, Varsity Lakes and Tugun
* $390 million to duplicate the North Coast line between Beerburrum and Landsborough
* $300 million for the Brisbane Metro
* $170 million for the Cunningham Highway, linking the Darling Downs and Ipswich
* $64.2 million for upgrades on the Warrego Highway
* Additional money via a $1.5 billion fund for Northern Australian roads
* Share of $160 million to improve sections of the Outback Way between Laverton in WA and Winton in Queensland
* $535.8 million over five years to help restore and protect the Great Barrier Reef.
